The long-term goal of the proposed research is to understand the developmental processes that regulate organ formation. This frequently involves asymmetric divisions of stem cells whose progeny take on new fates to specify cell types, which in turn progress down a pathway toward end-stage differentiation. In plants, the Arabidopsis root has emerged as a leading model for organogenesis. Asymmetric division of specific stem cells at the tip of the root is controlled by a finely orchestrated interplay between two transcription factors, SHORTROOT (SHR) and SCARECROW (SCR). At least two intersecting pathways appear to lead to asymmetric division of the stem cells that generate the ground tissue. Recent results indicate that one pathway depends directly on SHR and SCR binding to the promoters of genes encoding the cell cycle machinery. The other pathway involves a transcriptional cascade through a newly identified transcription factor subfamily of which BLUEJAY (BLJ) appears to play a central role. In both animals and plants the regulation of organogenesis depends heavily on transcriptional networks. A goal of this proposal is to identify the transcriptional networks that link SHR and SCR's early role in asymmetric cell division with cell specification and subsequent differentiation of the ground tissue. The working model is that after asymmetric division of the stem cell daughter, direct targets of SHR and SCR set in motion a transcriptional cascade that specifies the two ground tissue lineages, endodermis and cortex and ultimately results in the end-stage differentiation of both cell types. Direct targets of BLJ and other SHR/SCR downstream genes will be identified and then their direct targets will be characterized. High-resolution expression datasets will be used to identify co-regulated genes specific to either of the ground tissue lineages. From these clusters, transcriptional regulators will be identified and their role in regulating the developmental pathway tested. Quantitative modeling approaches will be used to analyze the clusters and identify linkages between regulatory units. Specific aims are to: 1) Identify and characterize the factors that work with SHR and SCR to regulate stem cell asymmetric divisions; 2) Characterize the networks that link asymmetric cell division to end- stage differentiation; 3) Model network connectivity along the differentiation pathway.